UC Irvine

Adaptation by natural selection is a fundamental process in evolution, yet there is a deficit in our understanding of the mechanisms of adaptation at the genomic level and how genetic changes translate to phenotypic change. For my dissertation, I addressed questions about evolution using genomic and experimental data to better understand the phenotypic and genotypic changes underlying adaptation and to investigate the consequences of adaptation utilizing bacteria as my study system.

In my first chapter, I investigated the mechanisms of adaptation that underlie evolutionary rescue in Escherichia coli. In my experiment, rescue occurred for 9% of populations, and I found that one mutation in either the rpoBC (RNA polymerase) or hslVU (heat shock protease) operon was sufficient for rescue. Overall, this chapter demonstrated that a single mutation in the rpoBC or hslVU operon allowed for rescue through similar changes in gene expression, and that adaptation by rescue may be qualitatively different from adaptation to non-lethal stress.

In my second chapter, I studied evolutionary contingency and its effects on adaptive potential. To study contingency, I expanded on a large evolution experiment previously conducted in the Gaut lab. In this experiment, over 100 originally identical populations of E. coli adapted to thermal stress (42.2°C) through two distinct pathways. By conducting a second evolution experiment in a novel thermal environment (19.0°C), I contrasted the evolution of a subset of the E. coli populations descended from either adaptive pathway. I found evidence to suggest that the adaptive history of a population may significantly influence future genotypic evolution and even phenotypic outcomes to an extent.

Finally, in my third chapter, I investigated the effects of evolution and adaptation on the genome of the plant pathogen Xylella fastidiosa. This bacterium causes devastating disease in many economically important crops around the world. Using maximum likelihood methods, I estimated the ratio of nonsynonymous to synonymous substitutions (dN/dS) in over 5,000 core and accessory genes found in the Xylella genus. By screening for positive selection using dN/dS, I identified both core and accessory genes that may affect pathogenicity, including genes involved in biofilm formation.